VizCNV

This is a shiny app for chromosomal copy number variant analysis. It can parse the vcf file with SV calls, visualize CNV and B-allele frequency and genetic phasing information interactively.

Prerequisites

R version >= 3.6.3 Following R libraries are required:

Shifting level models based segmentation is performed using SLMSuite.

Launch app on local with the main branch:

shiny::runGitHub(repo = "BCM-Lupskilab/VizCNV")

or Launch app on local with the dev branch:

shiny::runGitHub(repo = "cluhaowie/VizCNV",ref="dev")

A docker image is public available through docker hub docker pull duclare123/vizcnv_dev

Upload the required file from local file systerm:

If launch the app on cloud or on server, input file need to be upload due to access restriction.

Visualize the CNV calls in table format, read depth plot and B-allele frequency together:

The app require read depth file as the input: A output from mosedepth can be used example of generate the read depth file for 1Kb window size would be:

mosdepth -n --fast-mode --by 1000 sample.wgs $sample.wgs.cram